OEWG 20110830

OBO-Edit Working Group Meeting: Tuesday, August 30, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes:
Attendees:

Bug and Feature Trackers

• OE Bug tracker
• OE Feature tracker

Fixed since last meeting

• Heiko replaced the File Browser in OE with the native one so that you have the full browsing power of the Finder (and it remembers where you last browsed, which is also great). This is a fix for File browser in Mac OBO-Edit doesn't show second hard drive. The one small downside of the new File Browser is that you can't load multiple files at once (from the Basic Load interface), but OE users said that was ok, they didn't load multiple ontologies that way anyway (those who load multiple ontologies at once prefer to use the Advanced load with saved load profiles).
• Name Redundancy check doesn't work
  • Jane wrote, "I managed to commit two terms to GO which had identical names to existing terms this week, without the verification plugin objecting."
  • It turned out that the Verification Check for identical names was set to run "On text commit", which doesn't seem to work.
    • Added bug report for this: Checks run "on text commit" don't show warning messages
      • This is not generally an issue, because the Redundant Name Check was in fact the ONLY verification check that was set to run "On text commit" but not "During text edit".
  • I fixed this by making this check run "On text edit", and now you see a warning (in the Text Editor titlebar) if you give a term a name that another (non-obsolete) term has. (Like before, this is not a fatal error; it's a warning.)
  • Future feature request: Enable users to configure checks as warnings or errors
    • Note that this could be a way to mitigate this problem: fatal errors in ontologies that aren't yours preventing you from saving edits you've made to your ontology after loading multiple ontologies.

• obo2obo no longer prints status messages to stdout
• Quick fix for repeated words etc. adds to wrong file
  • The quick fixes were adding to files in oboedit_config instead of oboedit_config/dict (so Jane and other users had to add the fixes by hand)

• Fixing JUnit tests for OBO and OBO-Edit
  • Fixed some tests; removed some that Chris M. said were obsolete
  • 2.1-b18 now passes a lot more tests than 2.0
  • 2.0:
    • 21/43 OBO JUnit tests pass
    • 1/24 OBO-Edit JUnit tests pass
  • 2.1-b18:
    • 38/38 OBO JUnit tests pass
    • 10/24 OBO-Edit JUnit tests pass
      • None of the failures are new--all 14 that fail now also failed in 2.0.

Discussion Items

• New file browser had bug in b17--Heiko quickly fixed it and we released b18 the next day.
• Did anyone (other than Midori) get a chance to test obo2obo to make sure my fix for [ geneontology-Bugs-3316815 ] (filtered save doesn't save dangling parents) didn't break anything in obo2obo?
  • Midori found one issue in obo2obo but it turned out to be old and unimportant
  • Fixed problem where obo2obo recently stopped printing status messages to stdout.
  • The obo2obo tests I tried yielded the same output for OE 2.0 and 2.1-b18.

• Next meeting: we will skip Tuesday, September 6 and meet next on September 20.
• With a new academic year starting, should we revisit the meeting day/time or just keep it as it is?

Currently working on

• Working towards making an official 2.1 release

• Is_a closure broken
  • Midori commented, "I can confirm that I get the same thing (or at least something similar) happening with 'regulates' relationships: is_a closure saves some terms that would only be there if it followed at least one 'regulates' link.
  • Chris said "This has become a lower priority for OE, since we will be able to do most of this in Oort." Should I stop working on this?

Next bugs to work on

• check def dbxref for non-standard characters when saving

• Fixing any bugs that the JUnit tests reveal

Discussion

Links

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